[phenixbb] Where to find optimized wxc_scale/wxu_scale weighting factors after optimization

amadrona at uci.edu amadrona at uci.edu
Thu Aug 12 11:44:39 PDT 2010


>   Hi Yarow,
>
>> I ran a refinement optimizing geometry and B factor weighting factors
>> using optimize_wxc=true optimize_wxu=true.
>>
>> I was given these statistics in the pdb header:
>>
>>          Rwork   Rfree  Bonds  Angles
>> start  .1588    .1838   .007  1.235
>> end      .1454  .1780   .016  1.601
>>
>> (1.37 A resolution)
>
> Looks ok. Did you update solvent using "ordered_solvent=true"? Did you
> remember to add have H atoms to your structure?

Thanks Pavel,

No, I did not have these turned on.  It appears that
"ordered_solvent=true" is essentially a water checker in later stages of
refinement (correct me if I am wrong).  I will try turning this on.

What are the advantages of adding H atoms if you are not going to refine
them?  (Bear with me--this is my first structure).


>
>> 1.  I would like to find the optimized weighting factors in the log file
>> but cannot.  Instead I find the following (pasted below).
>
> I'm wondering why you are trying to find them? It is such a technical
> thing that changes from macro-cycle to macro-cycle...

I was attempting to use the best weighting factors in subsequent rounds of
refinement so that I did not have to optimize each time (because it takes
a long time to run).  Is this a good strategy?


>
>> However, the
>> scale here doesn't make sense to me because many our greater than 0.5.
>
> Hm... In the text below actually none of them is equal to 0.5. May be
> you meant ADP refinement?
>
>> How do I find the optimized values so that I can use them in further
>> rounds of refinement?
>
> See below.
>
>> 2.  Can anyone explain the concept of optimizing the B-factor?  I don't
>> understand how changing it brings you closer or further from an ideal
>> model as oppose to xray. (which is how I make sense of refining the
>> geometry)
>
> Start here ("On atomic displacement parameters (ADP)"):
> http://www.phenix-online.org/newsletter/CCN_2010_07.pdf
> and
> http://www.phenix-online.org/presentations/latest/pavel_refinement_general.pdf
> then may be have a look:
> http://www.phenix-online.org/presentations/latest/pavel_phenix_refine.pdf


Thank you!

>
>> ================================ xyz refinement
>> ===============================
>>
>> Start r_work= 0.1462 r_free= 0.1784 bonds= 0.015 angles=  1.53
>>        r_work= 0.1492 r_free= 0.1792 bonds= 0.005 angles=  1.08 scale=
>> 1.00
>>        r_work= 0.1484 r_free= 0.1788 bonds= 0.006 angles=  1.14 scale=
>> 1.40
>>        r_work= 0.1480 r_free= 0.1787 bonds= 0.007 angles=  1.19 scale=
>> 1.80
>>        r_work= 0.1476 r_free= 0.1785 bonds= 0.008 angles=  1.23 scale=
>> 2.20
>>        r_work= 0.1473 r_free= 0.1785 bonds= 0.008 angles=  1.26 scale=
>> 2.60
>>        r_work= 0.1471 r_free= 0.1784 bonds= 0.009 angles=  1.29 scale=
>> 3.00
>>        r_work= 0.1469 r_free= 0.1784 bonds= 0.010 angles=  1.32 scale=
>> 3.40
>>        r_work= 0.1467 r_free= 0.1783 bonds= 0.010 angles=  1.34 scale=
>> 3.80
>>        r_work= 0.1465 r_free= 0.1782 bonds= 0.011 angles=  1.36 scale=
>> 4.20
>>        r_work= 0.1464 r_free= 0.1782 bonds= 0.011 angles=  1.39 scale=
>> 4.60
>>        r_work= 0.1463 r_free= 0.1782 bonds= 0.011 angles=  1.40 scale=
>> 5.00
>>        r_work= 0.1461 r_free= 0.1781 bonds= 0.012 angles=  1.45 scale=
>> 6.00
>>        r_work= 0.1458 r_free= 0.1781 bonds= 0.013 angles=  1.49 scale=
>> 7.00
>>        r_work= 0.1456 r_free= 0.1781 bonds= 0.014 angles=  1.53 scale=
>> 8.00
>>        r_work= 0.1454 r_free= 0.1781 bonds= 0.015 angles=  1.57 scale=
>> 9.00
>>        r_work= 0.1453 r_free= 0.1780 bonds= 0.016 angles=  1.60 scale=
>> 10.00
>>        r_work= 0.1495 r_free= 0.1794 bonds= 0.005 angles=  1.05 scale=
>> 0.85
>>        r_work= 0.1501 r_free= 0.1797 bonds= 0.005 angles=  1.02 scale=
>> 0.70
>>        r_work= 0.1507 r_free= 0.1800 bonds= 0.004 angles=  0.98 scale=
>> 0.55
>> Final r_work= 0.1453 r_free= 0.1780 bonds= 0.016 angles=  1.60
>
> The optimal wxc_scale = 10.00, that corresponds to
> Final r_work= 0.1453 r_free= 0.1780 bonds= 0.016 angles= 1.60
>
> All the best!
> Pavel.
>
>





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